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Nagana Gowda GA, Raftery D. Analysis of Plasma, Serum, and Whole Blood Metabolites Using 1H NMR Spectroscopy. Methods Mol Biol 2019; 2037:17-34. [PMID: 31463837 DOI: 10.1007/978-1-4939-9690-2_2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Blood is the most widely used biological specimen in the metabolomics field. With its unique characteristics of high reproducibility and excellent quantitation, NMR spectroscopy offers immense benefits for the analysis of blood metabolites. In the metabolomics field, intact blood serum and plasma have been widely used for many years. However, such analysis has met with challenges arising from the deleterious effects of the abundant proteins in serum and plasma. Recent advances have led to the development of improved NMR methods that involve removal of protein before analysis. In particular, protein removal by precipitation using methanol alone or using a mixture of methanol and chloroform was shown to be an optimal method for metabolite recovery and for producing highly resolved NMR spectra. This has led to the absolute quantitation of nearly 70 metabolites in serum and plasma and nearly 80 in whole blood. In this chapter, we describe protocols for the analysis of blood serum, blood plasma, and whole blood metabolites using 1D 1H NMR spectroscopy methods.
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Affiliation(s)
- G A Nagana Gowda
- Northwest Metabolomics Research Center, University of Washington, Seattle, WA, USA.,Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA, USA.,Mitochondria and Metabolism Center, University of Washington, Seattle, WA, USA
| | - Daniel Raftery
- Northwest Metabolomics Research Center, University of Washington, Seattle, WA, USA. .,Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA, USA. .,Mitochondria and Metabolism Center, University of Washington, Seattle, WA, USA. .,Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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52
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Jasbi P, Wang D, Cheng SL, Fei Q, Cui JY, Liu L, Wei Y, Raftery D, Gu H. Breast cancer detection using targeted plasma metabolomics. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1105:26-37. [DOI: 10.1016/j.jchromb.2018.11.029] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 11/27/2018] [Accepted: 11/30/2018] [Indexed: 12/11/2022]
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53
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Zang X, Monge ME, Gaul DA, Fernández FM. Flow Injection–Traveling-Wave Ion Mobility–Mass Spectrometry for Prostate-Cancer Metabolomics. Anal Chem 2018; 90:13767-13774. [DOI: 10.1021/acs.analchem.8b04259] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Xiaoling Zang
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - María Eugenia Monge
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, Ciudad de Buenos Aires C1425FQD, Argentina
| | - David A. Gaul
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Facundo M. Fernández
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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54
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Gao P, da Silva E, Hou L, Denslow ND, Xiang P, Ma LQ. Human exposure to polycyclic aromatic hydrocarbons: Metabolomics perspective. ENVIRONMENT INTERNATIONAL 2018; 119:466-477. [PMID: 30032012 DOI: 10.1016/j.envint.2018.07.017] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/09/2018] [Accepted: 07/09/2018] [Indexed: 05/22/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are organic contaminants exhibiting carcinogenic toxicity. They are widespread in the environment, especially in urban areas. Humans are exposed to PAHs via inhalation, ingestion and dermal contact. Though much research has investigated their toxicity, little is known regarding the metabolic responses in humans after exposing to PAHs. However, those studies are important since PAHs become carcinogenic after metabolic activation by humans as indirect-acting carcinogens. As such, it is important to study their metabolism in humans based on metabolomics analysis. The goal of metabolomics study is to obtain a comprehensive view of metabolic reactions in humans after exposing to PAHs to better control the underlying metabolisms and reduce their genotoxicity. This article reviewed the biomarkers, analytical techniques including nuclear magnetic resonance and mass spectrometry, big data multivariate statistical analysis, and animal models that have been utilized to better understand the biological effects of PAHs, PAH-derivatives, and their metabolites and biotransformation products on humans.
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Affiliation(s)
- Peng Gao
- Research Center for Soil Contamination and Environment Remediation, Southwest Forestry University, Kunming 650224, China; Soil and Water Sciences Department, University of Florida, Gainesville, FL 32611, United States
| | - Evandro da Silva
- Soil and Water Sciences Department, University of Florida, Gainesville, FL 32611, United States
| | - Lei Hou
- Research Center for Soil Contamination and Environment Remediation, Southwest Forestry University, Kunming 650224, China
| | - Nancy D Denslow
- Department of Physiological Sciences, and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, United States
| | - Ping Xiang
- Research Center for Soil Contamination and Environment Remediation, Southwest Forestry University, Kunming 650224, China.
| | - Lena Q Ma
- Research Center for Soil Contamination and Environment Remediation, Southwest Forestry University, Kunming 650224, China; Soil and Water Sciences Department, University of Florida, Gainesville, FL 32611, United States.
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55
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Ng S, Strunk T, Jiang P, Muk T, Sangild PT, Currie A. Precision Medicine for Neonatal Sepsis. Front Mol Biosci 2018; 5:70. [PMID: 30094238 PMCID: PMC6070631 DOI: 10.3389/fmolb.2018.00070] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 07/06/2018] [Indexed: 11/24/2022] Open
Abstract
Neonatal sepsis remains a significant cause of morbidity and mortality especially in the preterm infant population. The ability to promptly and accurately diagnose neonatal sepsis based on clinical evaluation and laboratory blood tests remains challenging. Advances in high-throughput molecular technologies have increased investigations into the utility of transcriptomic, proteomic and metabolomic approaches as diagnostic tools for neonatal sepsis. A systems-level understanding of neonatal sepsis, obtained by using omics-based technologies (at the transcriptome, proteome or metabolome level), may lead to new diagnostic tools for neonatal sepsis. In particular, recent omic-based studies have identified distinct transcriptional signatures and metabolic or proteomic biomarkers associated with sepsis. Despite the emerging need for a systems biology approach, future studies have to address the challenges of integrating multi-omic data with laboratory and clinical meta-data in order to translate outcomes into precision medicine for neonatal sepsis. Omics-based analytical approaches may advance diagnostic tools for neonatal sepsis. More research is needed to validate the recent systems biology findings in order to integrate multi-dimensional data (clinical, laboratory and multi-omic) for future translation into precision medicine for neonatal sepsis. This review will discuss the possible applications of omics-based analyses for identification of new biomarkers and diagnostic signatures for neonatal sepsis, focusing on the immune-compromised preterm infant and considerations for clinical translation.
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Affiliation(s)
- Sherrianne Ng
- Medical and Molecular Sciences, School of Veterinary and Life Sciences, Murdoch University, Perth, WA, Australia
| | - Tobias Strunk
- Centre for Neonatal Research and Education, The University of Western Australia, Perth, WA, Australia
| | - Pingping Jiang
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Tik Muk
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Per T Sangild
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Andrew Currie
- Medical and Molecular Sciences, School of Veterinary and Life Sciences, Murdoch University, Perth, WA, Australia.,Centre for Neonatal Research and Education, The University of Western Australia, Perth, WA, Australia
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56
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Nagana Gowda GA, Barding GA, Dai J, Gu H, Margineantu DH, Hockenbery DM, Raftery D. A Metabolomics Study of BPTES Altered Metabolism in Human Breast Cancer Cell Lines. Front Mol Biosci 2018; 5:49. [PMID: 29868609 PMCID: PMC5962734 DOI: 10.3389/fmolb.2018.00049] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 04/24/2018] [Indexed: 12/11/2022] Open
Abstract
The Warburg effect is a well-known phenomenon in cancer, but the glutamine addiction in which cancer cells utilize glutamine as an alternative source of energy is less well known. Recent efforts have focused on preventing cancer cell proliferation associated with glutamine addiction by targeting glutaminase using the inhibitor BPTES (bis-2-(5-phenylacetamido-1,3,4-thiadiazol-2-yl)ethyl sulfide). In the current study, an investigation of the BPTES induced changes in metabolism was made in two human breast cancer cell lines, MCF7 (an estrogen receptor dependent cell line) and MDA-MB231 (a triple negative cell line), relative to the non-cancerous cell line, MCF10A. NMR spectroscopy combined with a recently established smart-isotope tagging approach enabled quantitative analysis of 41 unique metabolites representing numerous metabolite classes including carbohydrates, amino acids, carboxylic acids and nucleotides. BPTES induced metabolism changes in the cancer cell lines were especially pronounced under hypoxic conditions with up to 1/3 of the metabolites altered significantly (p < 0.05) relative to untreated cells. The BPTES induced changes were more pronounced for MCF7 cells, with 14 metabolites altered significantly (p < 0.05) compared to seven for MDA-MB231. Analyses of the results indicate that BPTES affected numerous metabolic pathways including glycolysis, TCA cycle, nucleotide and amino acid metabolism in cancer. The distinct metabolic responses to BPTES treatment determined in the two breast cancer cell lines offer valuable metabolic information for the exploration of the therapeutic responses to breast cancer.
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Affiliation(s)
- G A Nagana Gowda
- Department of Anesthesiology and Pain Medicine, Northwest Metabolomics Research Center, University of Washington, Seattle, WA, United States
| | - Gregory A Barding
- Department of Anesthesiology and Pain Medicine, Northwest Metabolomics Research Center, University of Washington, Seattle, WA, United States
| | - Jin Dai
- Department of Anesthesiology and Pain Medicine, Northwest Metabolomics Research Center, University of Washington, Seattle, WA, United States
| | - Haiwei Gu
- Department of Anesthesiology and Pain Medicine, Northwest Metabolomics Research Center, University of Washington, Seattle, WA, United States
| | | | | | - Daniel Raftery
- Department of Anesthesiology and Pain Medicine, Northwest Metabolomics Research Center, University of Washington, Seattle, WA, United States.,Fred Hutchinson Cancer Research Center, Seattle, WA, United States.,Department of Chemistry, University of Washington, Seattle, WA, United States
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57
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Davison J, O'Gorman A, Brennan L, Cotter DR. A systematic review of metabolite biomarkers of schizophrenia. Schizophr Res 2018; 195:32-50. [PMID: 28947341 DOI: 10.1016/j.schres.2017.09.021] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 09/01/2017] [Accepted: 09/14/2017] [Indexed: 12/23/2022]
Abstract
Current diagnosis of schizophrenia relies exclusively on the potentially subjective interpretation of clinical symptoms and social functioning as more objective biological measurement and medical diagnostic tests are not presently available. The use of metabolomics in the discovery of disease biomarkers has grown in recent years. Metabolomic methods could aid in the discovery of diagnostic biomarkers of schizophrenia. This systematic review focuses on biofluid metabolites associated with schizophrenia. A systematic search of Web of Science and Ovid Medline databases was conducted and 63 studies investigating metabolite biomarkers of schizophrenia were included. A review of these studies revealed several potential metabolite signatures of schizophrenia including reduced levels of essential polyunsaturated fatty acids (EPUFAs), vitamin E and creatinine; and elevated levels of lipid peroxidation metabolites and glutamate. Further research is needed to validate these biomarkers and would benefit from large cohort studies and more homogeneous and well-defined subject groups.
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Affiliation(s)
- Jennifer Davison
- RCSI Psychiatry, Royal College of Surgeons in Ireland, Education and Research Centre Beaumont Hospital, Dublin 9, Ireland; Institute of Food & Health, UCD School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland
| | - Aoife O'Gorman
- RCSI Psychiatry, Royal College of Surgeons in Ireland, Education and Research Centre Beaumont Hospital, Dublin 9, Ireland; Institute of Food & Health, UCD School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland
| | - Lorraine Brennan
- Institute of Food & Health, UCD School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland
| | - David R Cotter
- RCSI Psychiatry, Royal College of Surgeons in Ireland, Education and Research Centre Beaumont Hospital, Dublin 9, Ireland.
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58
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Isa F, Collins S, Lee MH, Decome D, Dorvil N, Joseph P, Smith L, Salerno S, Wells MT, Fischer S, Bean JM, Pape JW, Johnson WD, Fitzgerald DW, Rhee KY. Mass Spectrometric Identification of Urinary Biomarkers of Pulmonary Tuberculosis. EBioMedicine 2018; 31:157-165. [PMID: 29752217 PMCID: PMC6013777 DOI: 10.1016/j.ebiom.2018.04.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/04/2018] [Accepted: 04/17/2018] [Indexed: 02/02/2023] Open
Abstract
Background Tuberculosis (TB) is the leading infectious cause of death worldwide. A major barrier to control of the pandemic is a lack of clinical biomarkers with the ability to distinguish active TB from healthy and sick controls and potential for development into point-of-care diagnostics. Methods We conducted a prospective case control study to identify candidate urine-based diagnostic biomarkers of active pulmonary TB (discovery cohort) and obtained a separate blinded “validation” cohort of confirmed cases of active pulmonary TB and controls with non-tuberculous pulmonary disease for validation. Clean-catch urine samples were collected and analyzed using high performance liquid chromatography-coupled time-of-flight mass spectrometry. Results We discovered ten molecules from the discovery cohort with receiver-operator characteristic (ROC) area-under-the-curve (AUC) values >85%. These 10 molecules also significantly decreased after 60 days of treatment in a subset of 20 participants followed over time. Of these, a specific combination of diacetylspermine, neopterin, sialic acid, and N-acetylhexosamine exhibited ROC AUCs >80% in a blinded validation cohort of participants with active TB and non-tuberculous pulmonary disease. Conclusion Urinary levels of diacetylspermine, neopterin, sialic acid, and N-acetylhexosamine distinguished patients with tuberculosis from healthy controls and patients with non-tuberculous pulmonary diseases, providing a potential noninvasive biosignature of active TB. Funding This study was funded by Weill Cornell Medicine, the National Institute of Allergy and Infectious Diseases, the Clinical and Translational Science Center at Weill Cornell, the NIH Fogarty International Center grants, and the NIH Tuberculosis Research Unit (Tri-I TBRU). Urinary levels of small metabolites appear capable of distinguishing cases of active pulmonary tuberculosis from sick and healthy controls. Levels of these biomarkers decrease after 60 days of treatment in a longitudinal cohort of 20 participants. - Many of the identified biomarkers are known inflammatory intermediates that may reflect a specific immune response to tuberculosis.
Urine tests are commonly used to enable non-invasive, rapid and point-of-care diagnosis of various infectious diseases. We identified diacetylspermine, neopterin, sialic acid and N-acetylhexosamine as potential urine-based biomarkers for tuberculosis from two independent patient cohorts. These metabolites are known inflammatory intermediates and appear to decrease with anti-tuberculosis therapy in a subset of participants followed over 2 months. If validated, these metabolites have potential to both improve our understanding of the immune reaction to active tuberculosis and facilitate the development of a much-needed clinical biomarker for tuberculosis.
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Affiliation(s)
- Flonza Isa
- Department of Medicine, Weill Cornell Medicine, New York, NY, United States; Center for Global Health, Weill Cornell Medicine, New York, NY, United States
| | - Sean Collins
- Department of Medicine, Stanford Medicine, Stanford, CA, United States
| | - Myung Hee Lee
- Center for Global Health, Weill Cornell Medicine, New York, NY, United States
| | - Diessy Decome
- Groupe Haitien d'Etude du Sarcome de Kaposi et des Infections Opportunistes (GHESKIO), Port au Prince, Haiti
| | - Nancy Dorvil
- Groupe Haitien d'Etude du Sarcome de Kaposi et des Infections Opportunistes (GHESKIO), Port au Prince, Haiti
| | - Patrice Joseph
- Groupe Haitien d'Etude du Sarcome de Kaposi et des Infections Opportunistes (GHESKIO), Port au Prince, Haiti
| | | | - Stephen Salerno
- Department of Statistical Science, Cornell University, Ithaca, NY, United States
| | - Martin T Wells
- Department of Statistical Science, Cornell University, Ithaca, NY, United States
| | | | - James M Bean
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Jean W Pape
- Center for Global Health, Weill Cornell Medicine, New York, NY, United States; Groupe Haitien d'Etude du Sarcome de Kaposi et des Infections Opportunistes (GHESKIO), Port au Prince, Haiti
| | - Warren D Johnson
- Department of Medicine, Weill Cornell Medicine, New York, NY, United States; Center for Global Health, Weill Cornell Medicine, New York, NY, United States; Groupe Haitien d'Etude du Sarcome de Kaposi et des Infections Opportunistes (GHESKIO), Port au Prince, Haiti
| | - Daniel W Fitzgerald
- Department of Medicine, Weill Cornell Medicine, New York, NY, United States; Center for Global Health, Weill Cornell Medicine, New York, NY, United States; Groupe Haitien d'Etude du Sarcome de Kaposi et des Infections Opportunistes (GHESKIO), Port au Prince, Haiti
| | - Kyu Y Rhee
- Department of Medicine, Weill Cornell Medicine, New York, NY, United States; Center for Global Health, Weill Cornell Medicine, New York, NY, United States.
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59
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Makris K, Haliassos A, Chondrogianni M, Tsivgoulis G. Blood biomarkers in ischemic stroke: potential role and challenges in clinical practice and research. Crit Rev Clin Lab Sci 2018; 55:294-328. [DOI: 10.1080/10408363.2018.1461190] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Konstantinos Makris
- Clinical Biochemistry Department, KAT General Hospital, Kifissia, Athens, Greece
| | | | - Maria Chondrogianni
- Second Department of Neurology, Attikon Hospital, National and Kapodistrian University of Athens, School of Medicine, Athens, Greece
| | - Georgios Tsivgoulis
- Second Department of Neurology, Attikon Hospital, National and Kapodistrian University of Athens, School of Medicine, Athens, Greece
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60
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Abstract
Ischemic stroke is a sudden loss of brain function due to the reduction of blood flow. Brain tissues cease to function with subsequent activation of the ischemic cascade. Metabolomics and lipidomics are modern disciplines that characterize the metabolites and lipid components of a biological system, respectively. Because the pathogenesis of ischemic stroke is heterogeneous and multifactorial, it is crucial to establish comprehensive metabolomic and lipidomic approaches to elucidate these alterations in this disease. Fortunately, metabolomic and lipidomic studies have the distinct advantages of identifying tissue/mechanism-specific biomarkers, predicting treatment and clinical outcome, and improving our understanding of the pathophysiologic basis of disease states. Therefore, recent applications of these analytical approaches in the early diagnosis of ischemic stroke were discussed. In addition, the emerging roles of metabolomics and lipidomics on ischemic stroke were summarized, in order to gain new insights into the mechanisms underlying ischemic stroke and in the search for novel metabolite biomarkers and their related pathways.
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61
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Nagana Gowda GA, Djukovic D, Bettcher LF, Gu H, Raftery D. NMR-Guided Mass Spectrometry for Absolute Quantitation of Human Blood Metabolites. Anal Chem 2018; 90:2001-2009. [PMID: 29293320 DOI: 10.1021/acs.analchem.7b04089] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Broad-based, targeted metabolite profiling using mass spectrometry (MS) has become a major platform used in the field of metabolomics for a variety of applications. However, quantitative MS analysis is challenging owing to numerous factors including (1) the need for, ideally, isotope-labeled internal standards for each metabolite, (2) the fact that such standards may be unavailable or prohibitively costly, (3) the need to maintain the standards' concentrations close to those of the target metabolites, and (4) the alternative use of time-consuming calibration curves for each target metabolite. Here, we introduce a new method in which metabolites from a single serum specimen are quantified on the basis of a recently developed NMR method [ Nagana Gowda et al. Anal. Chem. 2015 , 87 , 706 ] and then used as references for absolute metabolite quantitation using MS. The MS concentrations of 30 metabolites thus derived for test serum samples exhibited excellent correlations with the NMR ones (R2 > 0.99) with a median CV of 3.2%. This NMR-guided-MS quantitation approach is simple and easy to implement and offers new avenues for the routine quantification of blood metabolites using MS. The demonstration that NMR and MS data can be compared and correlated when using identical sample preparations allows improved opportunities to exploit their combined strengths for biomarker discovery and unknown-metabolite identification. Intriguingly, however, metabolites including glutamine, pyroglutamic acid, glucose, and sarcosine correlated poorly with NMR data because of stability issues in their MS analyses or weak or overlapping signals. Such information is potentially important for improving biomarker discovery and biological interpretations. Further, the new quantitation method demonstrated here for human blood serum can in principle be extended to a variety of biological mixtures.
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Affiliation(s)
| | | | | | | | - Daniel Raftery
- Fred Hutchinson Cancer Research Center , Seattle, Washington 98109, United States
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62
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Luque de Castro M, Priego-Capote F. The analytical process to search for metabolomics biomarkers. J Pharm Biomed Anal 2018; 147:341-349. [DOI: 10.1016/j.jpba.2017.06.073] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 06/19/2017] [Accepted: 06/19/2017] [Indexed: 01/01/2023]
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63
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Marshall DD, Powers R. Beyond the paradigm: Combining mass spectrometry and nuclear magnetic resonance for metabolomics. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 100:1-16. [PMID: 28552170 PMCID: PMC5448308 DOI: 10.1016/j.pnmrs.2017.01.001] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 01/04/2017] [Accepted: 01/08/2017] [Indexed: 05/02/2023]
Abstract
Metabolomics is undergoing tremendous growth and is being employed to solve a diversity of biological problems from environmental issues to the identification of biomarkers for human diseases. Nuclear magnetic resonance (NMR) and mass spectrometry (MS) are the analytical tools that are routinely, but separately, used to obtain metabolomics data sets due to their versatility, accessibility, and unique strengths. NMR requires minimal sample handling without the need for chromatography, is easily quantitative, and provides multiple means of metabolite identification, but is limited to detecting the most abundant metabolites (⩾1μM). Conversely, mass spectrometry has the ability to measure metabolites at very low concentrations (femtomolar to attomolar) and has a higher resolution (∼103-104) and dynamic range (∼103-104), but quantitation is a challenge and sample complexity may limit metabolite detection because of ion suppression. Consequently, liquid chromatography (LC) or gas chromatography (GC) is commonly employed in conjunction with MS, but this may lead to other sources of error. As a result, NMR and mass spectrometry are highly complementary, and combining the two techniques is likely to improve the overall quality of a study and enhance the coverage of the metabolome. While the majority of metabolomic studies use a single analytical source, there is a growing appreciation of the inherent value of combining NMR and MS for metabolomics. An overview of the current state of utilizing both NMR and MS for metabolomics will be presented.
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Affiliation(s)
- Darrell D Marshall
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States.
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64
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Dysregulation of lipids in Alzheimer's disease and their role as potential biomarkers. Alzheimers Dement 2017; 13:810-827. [PMID: 28242299 DOI: 10.1016/j.jalz.2017.01.008] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 11/17/2016] [Accepted: 01/03/2017] [Indexed: 12/14/2022]
Abstract
The brain is highly enriched in lipids, and an intensive study of these lipids may be informative, not only of normal brain function but also of changes with age and in disease. In recent years, the development of highly sensitive mass spectrometry platforms and other high-throughput technologies has enabled the discovery of complex changes in the entire lipidome. This lipidomics approach promises to be a particularly useful tool for identifying diagnostic biomarkers for early detection of age-related neurodegenerative disease, such as Alzheimer's disease (AD), which has till recently been limited to protein- and gene-centric approaches. This review highlights known lipid changes affecting the AD brain and presents an update on the progress of lipid biomarker research in AD. Important considerations for designing large-scale lipidomics experiments are discussed to help standardize findings across different laboratories, as well as challenges associated with moving toward clinical application.
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65
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Watrous JD, Henglin M, Claggett B, Lehmann KA, Larson MG, Cheng S, Jain M. Visualization, Quantification, and Alignment of Spectral Drift in Population Scale Untargeted Metabolomics Data. Anal Chem 2017; 89:1399-1404. [PMID: 28208263 PMCID: PMC5455767 DOI: 10.1021/acs.analchem.6b04337] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Untargeted liquid-chromatography-mass spectrometry (LC-MS)-based metabolomics analysis of human biospecimens has become among the most promising strategies for probing the underpinnings of human health and disease. Analysis of spectral data across population scale cohorts, however, is precluded by day-to-day nonlinear signal drifts in LC retention time or batch effects that complicate comparison of thousands of untargeted peaks. To date, there exists no efficient means of visualization and quantitative assessment of signal drift, correction of drift when present, and automated filtering of unstable spectral features, particularly across thousands of data files in population scale experiments. Herein, we report the development of a set of R-based scripts that allow for pre- and postprocessing of raw LC-MS data. These methods can be integrated with existing data analysis workflows by providing initial preprocessing bulk nonlinear retention time correction at the raw data level. Further, this approach provides postprocessing visualization and quantification of peak alignment accuracy, as well as peak-reliability-based parsing of processed data through hierarchical clustering of signal profiles. In a metabolomics data set derived from ∼3000 human plasma samples, we find that application of our alignment tools resulted in substantial improvement in peak alignment accuracy, automated data filtering, and ultimately statistical power for detection of metabolite correlates of clinical measures. These tools will enable metabolomics studies of population scale cohorts.
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Affiliation(s)
- Jeramie D. Watrous
- Departments of Medicine and Pharmacology, University of California San Diego, La Jolla, California 92093, United States
| | - Mir Henglin
- Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Brian Claggett
- Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Kim A. Lehmann
- Departments of Medicine and Pharmacology, University of California San Diego, La Jolla, California 92093, United States
| | - Martin G. Larson
- Framingham Heart Study, Framingham, Massachusetts 01702, United States
- Biostatistics Department, School of Public Health, Boston University, Boston, Massachusetts 02118, United States
| | - Susan Cheng
- Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Framingham Heart Study, Framingham, Massachusetts 01702, United States
| | - Mohit Jain
- Departments of Medicine and Pharmacology, University of California San Diego, La Jolla, California 92093, United States
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Deng L, Gu H, Zhu J, Nagana Gowda GA, Djukovic D, Chiorean EG, Raftery D. Combining NMR and LC/MS Using Backward Variable Elimination: Metabolomics Analysis of Colorectal Cancer, Polyps, and Healthy Controls. Anal Chem 2016; 88:7975-83. [PMID: 27437783 DOI: 10.1021/acs.analchem.6b00885] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Both nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS) play important roles in metabolomics. The complementary features of NMR and MS make their combination very attractive; however, currently the vast majority of metabolomics studies use either NMR or MS separately, and variable selection that combines NMR and MS for biomarker identification and statistical modeling is still not well developed. In this study focused on methodology, we developed a backward variable elimination partial least-squares discriminant analysis algorithm embedded with Monte Carlo cross validation (MCCV-BVE-PLSDA), to combine NMR and targeted liquid chromatography (LC)/MS data. Using the metabolomics analysis of serum for the detection of colorectal cancer (CRC) and polyps as an example, we demonstrate that variable selection is vitally important in combining NMR and MS data. The combined approach was better than using NMR or LC/MS data alone in providing significantly improved predictive accuracy in all the pairwise comparisons among CRC, polyps, and healthy controls. Using this approach, we selected a subset of metabolites responsible for the improved separation for each pairwise comparison, and we achieved a comprehensive profile of altered metabolite levels, including those in glycolysis, the TCA cycle, amino acid metabolism, and other pathways that were related to CRC and polyps. MCCV-BVE-PLSDA is straightforward, easy to implement, and highly useful for studying the contribution of each individual variable to multivariate statistical models. On the basis of these results, we recommend using an appropriate variable selection step, such as MCCV-BVE-PLSDA, when analyzing data from multiple analytical platforms to obtain improved statistical performance and a more accurate biological interpretation, especially for biomarker discovery. Importantly, the approach described here is relatively universal and can be easily expanded for combination with other analytical technologies.
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Affiliation(s)
- Lingli Deng
- Department of Information Engineering, East China University of Technology , 418 Guanglan Avenue, Nanchang, Jiangxi Province 330013, China.,Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington , 850 Republican Street, Seattle, Washington 98109, United States
| | - Haiwei Gu
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington , 850 Republican Street, Seattle, Washington 98109, United States.,Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology , 418 Guanglan Avenue, Nanchang, Jiangxi Province 330013, China
| | - Jiangjiang Zhu
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington , 850 Republican Street, Seattle, Washington 98109, United States
| | - G A Nagana Gowda
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington , 850 Republican Street, Seattle, Washington 98109, United States
| | - Danijel Djukovic
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington , 850 Republican Street, Seattle, Washington 98109, United States
| | - E Gabriela Chiorean
- Department of Medicine, University of Washington , 825 Eastlake Avenue East, Seattle, Washington 98109, United States.,Indiana University Melvin and Bren Simon Cancer Center , 535 Barnhill Drive, Indianapolis, Indiana 46202, United States
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington , 850 Republican Street, Seattle, Washington 98109, United States.,Department of Chemistry, Purdue University , 560 Oval Drive, West Lafayette, Indiana 47907, United States.,Public Health Sciences Division, Fred Hutchinson Cancer Research Center , 1100 Fairview Avenue North, Seattle, Washington 98109, United States
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Gu H, Zhang P, Zhu J, Raftery D. Globally Optimized Targeted Mass Spectrometry: Reliable Metabolomics Analysis with Broad Coverage. Anal Chem 2015; 87:12355-62. [PMID: 26579731 PMCID: PMC5437843 DOI: 10.1021/acs.analchem.5b03812] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Targeted detection is one of the most important methods in mass spectrometry (MS)-based metabolomics; however, its major limitation is the reduced metabolome coverage that results from the limited set of targeted metabolites typically used in the analysis. In this study we describe a new approach, globally optimized targeted (GOT)-MS, that combines many of the advantages of targeted detection and global profiling in metabolomics analysis, including the capability to detect unknowns, broad metabolite coverage, and excellent quantitation. The key step in GOT-MS is a global search of precursor and product ions using a single liquid chromatography-triple quadrupole (LC-QQQ) mass spectrometer. Here, focused on measuring serum metabolites, we obtained 595 precursor ions and 1 890 multiple reaction monitoring (MRM) transitions, under positive and negative ionization modes in the mass range of 60-600 Da. For many of the MRMs/metabolites under investigation, the analytical performance of GOT-MS is better than or at least comparable to that obtained by global profiling using a quadrupole-time-of-flight (Q-TOF) instrument of similar vintage. Using a study of serum metabolites in colorectal cancer (CRC) as a representative example, GOT-MS significantly outperformed a large targeted MS assay containing ∼160 biologically important metabolites and provided a complementary approach to traditional global profiling using Q-TOF-MS. GOT-MS thus expands and optimizes the detection capabilities for QQQ-MS through a novel approach and should have the potential to significantly advance both basic and clinical metabolic research.
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Affiliation(s)
- Haiwei Gu
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, Washington 98109, United States
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China Institute of Technology, Nanchang, Jiangxi Province 330013, P. R. China
| | - Ping Zhang
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, Washington 98109, United States
- Department of Applied Chemistry, China Agricultural University, Beijing 100193, P.R. China
| | - Jiangjiang Zhu
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, Washington 98109, United States
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, Washington 98109, United States
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, United States
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Nagana Gowda GA, Raftery D. Can NMR solve some significant challenges in metabolomics? JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 260:144-60. [PMID: 26476597 PMCID: PMC4646661 DOI: 10.1016/j.jmr.2015.07.014] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Revised: 07/17/2015] [Accepted: 07/18/2015] [Indexed: 05/04/2023]
Abstract
The field of metabolomics continues to witness rapid growth driven by fundamental studies, methods development, and applications in a number of disciplines that include biomedical science, plant and nutrition sciences, drug development, energy and environmental sciences, toxicology, etc. NMR spectroscopy is one of the two most widely used analytical platforms in the metabolomics field, along with mass spectrometry (MS). NMR's excellent reproducibility and quantitative accuracy, its ability to identify structures of unknown metabolites, its capacity to generate metabolite profiles using intact bio-specimens with no need for separation, and its capabilities for tracing metabolic pathways using isotope labeled substrates offer unique strengths for metabolomics applications. However, NMR's limited sensitivity and resolution continue to pose a major challenge and have restricted both the number and the quantitative accuracy of metabolites analyzed by NMR. Further, the analysis of highly complex biological samples has increased the demand for new methods with improved detection, better unknown identification, and more accurate quantitation of larger numbers of metabolites. Recent efforts have contributed significant improvements in these areas, and have thereby enhanced the pool of routinely quantifiable metabolites. Additionally, efforts focused on combining NMR and MS promise opportunities to exploit the combined strength of the two analytical platforms for direct comparison of the metabolite data, unknown identification and reliable biomarker discovery that continue to challenge the metabolomics field. This article presents our perspectives on the emerging trends in NMR-based metabolomics and NMR's continuing role in the field with an emphasis on recent and ongoing research from our laboratory.
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Affiliation(s)
- G A Nagana Gowda
- Northwest Metabolomics Research Center, Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98109, United States
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98109, United States; Department of Chemistry, University of Washington, Seattle, WA 98195, United States; Fred Hutchinson Cancer Research Center, Seattle, WA 98109, United States.
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Gowda GAN, Djukovic D. Overview of mass spectrometry-based metabolomics: opportunities and challenges. Methods Mol Biol 2015; 1198:3-12. [PMID: 25270919 DOI: 10.1007/978-1-4939-1258-2_1] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The field of metabolomics has witnessed an exponential growth in the last decade driven by important applications spanning a wide range of areas in the basic and life sciences and beyond. Mass spectrometry in combination with chromatography and nuclear magnetic resonance are the two major analytical avenues for the analysis of metabolic species in complex biological mixtures. Owing to its inherent significantly higher sensitivity and fast data acquisition, MS plays an increasingly dominant role in the metabolomics field. Propelled by the need to develop simple methods to diagnose and manage the numerous and widespread human diseases, mass spectrometry has witnessed tremendous growth with advances in instrumentation, experimental methods, software, and databases. In response, the metabolomics field has moved far beyond qualitative methods and simple pattern recognition approaches to a range of global and targeted quantitative approaches that are now routinely used and provide reliable data, which instill greater confidence in the derived inferences. Powerful isotope labeling and tracing methods have become very popular. The newly emerging ambient ionization techniques such as desorption ionization and rapid evaporative ionization have allowed direct MS analysis in real time, as well as new MS imaging approaches. While the MS-based metabolomics has provided insights into metabolic pathways and fluxes, and metabolite biomarkers associated with numerous diseases, the increasing realization of the extremely high complexity of biological mixtures underscores numerous challenges including unknown metabolite identification, biomarker validation, and interlaboratory reproducibility that need to be dealt with for realization of the full potential of MS-based metabolomics. This chapter provides a glimpse at the current status of the mass spectrometry-based metabolomics field highlighting the opportunities and challenges.
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Affiliation(s)
- G A Nagana Gowda
- Northwest Metabolomics Research Center, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA,
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Nagana Gowda GA, Gowda YN, Raftery D. Massive glutamine cyclization to pyroglutamic acid in human serum discovered using NMR spectroscopy. Anal Chem 2015; 87:3800-5. [PMID: 25746059 DOI: 10.1021/ac504435b] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Glutamine is one of the most abundant metabolites in blood and is a precursor as well as end product central to numerous important metabolic pathways. A number of surprising and unexpected roles for glutamine, including cancer cell glutamine addiction discovered recently, stress the importance of accurate analysis of glutamine concentrations for understanding its role in health and numerous diseases. Utilizing a recently developed NMR approach that offers access to an unprecedented number of quantifiable blood metabolites, we have identified a surprising glutamine cyclization to pyroglutamic acid that occurs during protein removal. Intact, ultrafiltered and protein precipitated samples from the same pool of human serum were comprehensively investigated using (1)H NMR spectroscopy at 800 MHz to detect and quantitatively evaluate the phenomenon. Interestingly, although glutamine cyclization occurs in both ultrafiltered and protein precipitated serum, the cyclization was not detected in intact serum. Strikingly, due to cyclization, the apparent serum glutamine level drops by up to 75% and, concomitantly, the pyroglutamic acid level increases proportionately. Further, virtually under identical conditions, the magnitude of cyclization is vastly different for different portions of samples from the same pool of human serum. However, the sum of glutamine and pyroglutamic acid concentrations in each sample remains the same for all portions. These unexpected findings indicate the importance of considering the sum of apparent glutamine and pyroglutamic acid levels, obtained from the contemporary analytical methods, as the actual blood glutamine level for biomarker discovery and biological interpretations.
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Affiliation(s)
| | | | - Daniel Raftery
- §Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
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Nagana Gowda GA, Gowda YN, Raftery D. Expanding the limits of human blood metabolite quantitation using NMR spectroscopy. Anal Chem 2014; 87:706-15. [PMID: 25485990 PMCID: PMC4287831 DOI: 10.1021/ac503651e] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
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A current challenge in metabolomics
is the reliable quantitation
of many metabolites. Limited resolution and sensitivity combined with
the challenges associated with unknown metabolite identification have
restricted both the number and the quantitative accuracy of blood
metabolites. Focused on alleviating this bottleneck in NMR-based metabolomics,
investigations of pooled human serum combining an array of 1D/2D NMR
experiments at 800 MHz, database searches, and spiking with authentic
compounds enabled the identification of 67 blood metabolites. Many
of these (∼1/3) are new compared with those reported previously
as a part of the Human Serum Metabolome Database. In addition, considering
both the high reproducibility and quantitative nature of NMR as well
as the sensitivity of NMR chemical shifts to altered sample conditions,
experimental protocols and comprehensive peak annotations are provided
here as a guide for identification and quantitation of the new pool
of blood metabolites for routine applications. Further, investigations
focused on the evaluation of quantitation using organic solvents revealed
a surprisingly poor performance for protein precipitation using acetonitrile.
One-third of the detected metabolites were attenuated by 10–67%
compared with methanol precipitation at the same solvent-to-serum
ratio of 2:1 (v/v). Nearly 2/3 of the metabolites were further attenuated
by up to 65% upon increasing the acetonitrile-to-serum ratio to 4:1
(v/v). These results, combined with the newly established identity
for many unknown metabolites in the NMR spectrum, offer new avenues
for human serum/plasma-based metabolomics. Further, the ability to
quantitatively evaluate nearly 70 blood metabolites that represent
numerous classes, including amino acids, organic acids, carbohydrates,
and heterocyclic compounds, using a simple and highly reproducible
analytical method such as NMR may potentially guide the evaluation
of samples for analysis using mass spectrometry.
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Affiliation(s)
- G A Nagana Gowda
- Northwest Metabolomics Research Center, Anesthesiology and Pain Medicine, and ‡Department of Chemistry, University of Washington , Seattle, Washington 98109, United States
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Gowda GAN, Raftery D. Quantitating metabolites in protein precipitated serum using NMR spectroscopy. Anal Chem 2014; 86:5433-40. [PMID: 24796490 PMCID: PMC4045325 DOI: 10.1021/ac5005103] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 05/05/2014] [Indexed: 01/04/2023]
Abstract
Quantitative NMR-based metabolite profiling is challenged by the deleterious effects of abundant proteins in the intact blood plasma/serum, which underscores the need for alternative approaches. Protein removal by ultrafiltration using low molecular weight cutoff filters thus represents an important step. However, protein precipitation, an alternative and simple approach for protein removal, lacks detailed quantitative assessment for use in NMR based metabolomics. In this study, we have comprehensively evaluated the performance of protein precipitation using methanol, acetonitrile, perchloric acid, and trichloroacetic acid and ultrafiltration approaches using 1D and 2D NMR, based on the identification and absolute quantitation of 44 human blood metabolites, including a few identified for the first time in the NMR spectra of human serum. We also investigated the use of a "smart isotope tag," (15)N-cholamine for further resolution enhancement, which resulted in the detection of a number of additional metabolites. (1)H NMR of both protein precipitated and ultrafiltered serum detected all 44 metabolites with comparable reproducibility (average CV, 3.7% for precipitation; 3.6% for filtration). However, nearly half of the quantified metabolites in ultrafiltered serum exhibited 10-74% lower concentrations; specifically, tryptophan, benzoate, and 2-oxoisocaproate showed much lower concentrations compared to protein precipitated serum. These results indicate that protein precipitation using methanol offers a reliable approach for routine NMR-based metabolomics of human blood serum/plasma and should be considered as an alternative to ultrafiltration. Importantly, protein precipitation, which is commonly used by mass spectrometry (MS), promises avenues for direct comparison and correlation of metabolite data obtained from the two analytical platforms to exploit their combined strength in the metabolomics of blood.
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Affiliation(s)
- G. A. Nagana Gowda
- Northwest Metabolomics
Research Center, Anesthesiology and Pain Medicine, and Department of
Chemistry, University of Washington, Seattle, Washington 98109, United States
| | - Daniel Raftery
- Northwest Metabolomics
Research Center, Anesthesiology and Pain Medicine, and Department of
Chemistry, University of Washington, Seattle, Washington 98109, United States
- Fred Hutchinson
Cancer Research Center, Seattle, Washington 98109, United States
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Gowda GAN, Djukovic D. Overview of mass spectrometry-based metabolomics: opportunities and challenges. Methods Mol Biol 2014; 1198:3-12. [PMID: 25270919 DOI: 10.1007/978-1-4939-1258-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The field of metabolomics has witnessed an exponential growth in the last decade driven by important applications spanning a wide range of areas in the basic and life sciences and beyond. Mass spectrometry in combination with chromatography and nuclear magnetic resonance are the two major analytical avenues for the analysis of metabolic species in complex biological mixtures. Owing to its inherent significantly higher sensitivity and fast data acquisition, MS plays an increasingly dominant role in the metabolomics field. Propelled by the need to develop simple methods to diagnose and manage the numerous and widespread human diseases, mass spectrometry has witnessed tremendous growth with advances in instrumentation, experimental methods, software, and databases. In response, the metabolomics field has moved far beyond qualitative methods and simple pattern recognition approaches to a range of global and targeted quantitative approaches that are now routinely used and provide reliable data, which instill greater confidence in the derived inferences. Powerful isotope labeling and tracing methods have become very popular. The newly emerging ambient ionization techniques such as desorption ionization and rapid evaporative ionization have allowed direct MS analysis in real time, as well as new MS imaging approaches. While the MS-based metabolomics has provided insights into metabolic pathways and fluxes, and metabolite biomarkers associated with numerous diseases, the increasing realization of the extremely high complexity of biological mixtures underscores numerous challenges including unknown metabolite identification, biomarker validation, and interlaboratory reproducibility that need to be dealt with for realization of the full potential of MS-based metabolomics. This chapter provides a glimpse at the current status of the mass spectrometry-based metabolomics field highlighting the opportunities and challenges.
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Affiliation(s)
- G A Nagana Gowda
- Northwest Metabolomics Research Center, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA,
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Nagana Gowda G, Raftery D. Advances in NMR-Based Metabolomics. FUNDAMENTALS OF ADVANCED OMICS TECHNOLOGIES: FROM GENES TO METABOLITES 2014. [DOI: 10.1016/b978-0-444-62651-6.00008-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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